5-29448886-C-T

Variant names:

• chr5-29448886-C-T
• rs684609

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.542 in 151,946 control chromosomes in the GnomAD database, including 23,734 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (23734 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82368 AN: 151824 Hom.: 23723 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.0845

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.575

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.542 AC: 82397 AN: 151946 Hom.: 23734 Cov.: 31 AF XY: 0.543 AC XY: 40294 AN XY: 74248

African (AFR) AF: 0.418 AC: 17319 AN: 41424

American (AMR) AF: 0.565 AC: 8636 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2139 AN: 3470

East Asian (EAS) AF: 0.0847 AC: 437 AN: 5160

South Asian (SAS) AF: 0.476 AC: 2289 AN: 4812

European-Finnish (FIN) AF: 0.688 AC: 7250 AN: 10542

Middle Eastern (MID) AF: 0.703 AC: 204 AN: 290

European-Non Finnish (NFE) AF: 0.624 AC: 42395 AN: 67948

Other (OTH) AF: 0.568 AC: 1199 AN: 2110

Alfa AF: 0.582 Hom.: 3167

Bravo AF: 0.527

Asia WGS AF: 0.275 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.68
DANN	Benign	0.35
PhyloP100		-0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs684609; hg19: chr5-29448993;